The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation-Reference-Cited by-同舟云学术

The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation

Published:2023-06-01 Issue:3 Volume:21 Page:483-500
ISSN:1672-0229
Container-title:Genomics, Proteomics & Bioinformatics
language:en
Short-container-title:

Author:

Chang Guobin¹²^ORCID,Yuan Xiaoya¹^ORCID,Guo Qixin¹^ORCID,Bai Hao²^ORCID,Cao Xiaofang³^ORCID,Liu Meng³^ORCID,Wang Zhixiu¹^ORCID,Li Bichun¹^ORCID,Wang Shasha¹^ORCID,Jiang Yong¹^ORCID,Wang Zhiquan⁴^ORCID,Zhang Yang¹^ORCID,Xu Qi¹^ORCID,Song Qianqian¹^ORCID,Pan Rui¹^ORCID,Qiu Lingling¹^ORCID,Gu Tiantian¹^ORCID,Wu Xinsheng¹^ORCID,Bi Yulin¹^ORCID,Cao Zhengfeng¹^ORCID,Zhang Yu¹^ORCID,Chen Yang¹^ORCID,Li Hong³^ORCID,Liu Jianfeng⁵^ORCID,Dai Wangcheng⁶^ORCID,Chen Guohong¹²^ORCID

Affiliation:

1. Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University , Yangzhou 225009 , China

2. Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou 225009 , China

3. Novogene Bioinformatics Institute , Beijing 100080 , China

4. Department of Agricultural, Food, and Nutritional Sciences, University of Alberta , Edmonton, AB T6G 2R3 , Canada

5. College of Animal Science and Technology, China Agricultural University , Beijing 100091 , China

6. Zhenjiang Tiancheng Agricultural Science and Technology Co., Ltd , Zhenjiang 210034 , China

Abstract

Abstract The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assemblies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.

Funder

China Agriculture Research System

Jiangsu Agricultural Technology System

Jiangsu Agricultural Science and Technology Innovation Fund

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Genetics,Molecular Biology,Biochemistry

Link

https://academic.oup.com/gpb/article-pdf/21/3/483/56416621/gpb_21_3_483.pdf

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